The “inverse modelling through iterative forward modelling” (IMIFM) approach is used to reconstruct the last deglaciation climates from central equatorial African mountains. Unlike other approaches that use statistical models, it directly incorporates the effects of changes in atmospheric CO2 concentrations on vegetation through a process-based vegetation model, but the results strongly depend on the model used. Therefore, two generally related but different equilibrium vegetation models are used for evaluating the dependence of the results on the choice of vegetation model. Our climate reconstructions show that long-term temperature increases during the last deglaciation, as seen in Greenland, were absent from many of the target sites. Moreover, there are few common long-term trends of climatic responses during the last deglaciation among central equatorial African mountains’ sites despite the relatively close of those sites. No systematic climate responses were also found between the eastern and western sides of the Congo basin. While there is consistency in the long-term trends and their amplitudes regarding temperature reconstructions with both models, there are large differences between the sites in the long-term hydroclimatic reconstructions, particularly during arid periods. This difference may be attributed to the carbon-water use efficiency in the vegetation models. This study implies that the IMIFM approach is effective for climate reconstructions in equatorial African mountains, where modern pollen samples are not plentiful. Although low atmospheric CO2 concentrations do not largely influence temperature reconstructions for the last deglaciation, they significantly affect the hydroclimate reconstructions, especially when drought-tolerant biomes are dominant.